SMTL ID : 3fz6.1

Crystal structure of glutamate decarboxylase beta from Escherichia coli: complex with xenon

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.82 Å

Oligo State

homo-hexamer

Ligands

6 x PMP: 4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE(Non-covalent)

PMP.1: 17 residues within 4Å: Chain A: G.125, S.126, S.127, Q.163, C.165, T.208, G.210, T.212, D.243, A.245, S.273, H.275, K.276, H.465, T.466 Chain B: F.317, S.318 14 PLIP interactions: 11 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:Q.163, A:T.208, A:A.245 Hydrogen bonds: A:S.126, A:S.127, A:Q.163, A:T.212, A:S.273, A:T.466, B:F.317, B:S.318, B:S.318 Salt bridges: A:H.275, A:K.276 PMP.3: 17 residues within 4Å: Chain A: F.317, S.318 Chain B: G.125, S.126, S.127, Q.163, C.165, T.208, G.210, T.212, D.243, A.245, S.273, H.275, K.276, H.465, T.466 16 PLIP interactions: 15 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:Q.163, B:T.208, B:A.245 Hydrogen bonds: B:S.126, B:S.127, B:Q.163, B:S.273, B:K.276, B:T.466, B:T.466, A:S.318 Water bridges: B:G.125, B:E.128, B:Q.163 Salt bridges: B:H.275, B:K.276 PMP.5: 16 residues within 4Å: Chain C: G.125, S.126, S.127, Q.163, C.165, T.208, T.212, D.243, A.245, S.273, H.275, K.276, H.465, T.466 Chain D: F.317, S.318 14 PLIP interactions: 12 interactions with chain C, 2 interactions with chain D Hydrophobic interactions: C:Q.163, C:Q.163, C:T.208 Hydrogen bonds: C:S.126, C:S.127, C:Q.163, C:T.212, C:S.273, C:T.466, D:F.317, D:S.318 Water bridges: C:Q.163 Salt bridges: C:H.275, C:K.276 PMP.7: 16 residues within 4Å: Chain C: F.317, S.318 Chain D: G.125, S.126, S.127, Q.163, C.165, T.208, T.212, D.243, A.245, S.273, H.275, K.276, H.465, T.466 16 PLIP interactions: 15 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:Q.163, D:Q.163, D:T.208, D:A.245 Hydrogen bonds: D:S.126, D:S.127, D:T.212, D:T.212, D:S.273, D:T.466, D:T.466, C:S.318 Water bridges: D:G.125, D:E.128 Salt bridges: D:H.275, D:K.276 PMP.9: 17 residues within 4Å: Chain E: G.125, S.126, S.127, Q.163, C.165, T.208, G.210, T.212, D.243, A.245, S.273, H.275, K.276, H.465, T.466 Chain F: F.317, S.318 16 PLIP interactions: 14 interactions with chain E, 2 interactions with chain F Hydrophobic interactions: E:Q.163, E:T.208, E:A.245 Hydrogen bonds: E:S.126, E:S.127, E:S.273, E:K.276, E:T.466, E:T.466, E:T.466, F:F.317, F:S.318 Water bridges: E:G.125, E:E.128 Salt bridges: E:H.275, E:K.276 PMP.11: 17 residues within 4Å: Chain E: F.317, S.318 Chain F: G.125, S.126, S.127, Q.163, C.165, T.208, G.210, T.212, D.243, A.245, S.273, H.275, K.276, H.465, T.466 14 PLIP interactions: 12 interactions with chain F, 2 interactions with chain E Hydrophobic interactions: F:Q.163, F:T.208, F:A.245 Hydrogen bonds: F:S.126, F:S.127, F:Q.163, F:T.212, F:T.212, F:T.466, F:T.466, E:F.317, E:S.318 Salt bridges: F:H.275, F:K.276

6 x XE: XENON(Non-covalent)

XE.2: 2 residues within 4Å: Chain A: G.120, L.295 No protein-ligand interaction detected (PLIP) XE.4: 3 residues within 4Å: Chain B: G.120, L.295, F.313 No protein-ligand interaction detected (PLIP) XE.6: 2 residues within 4Å: Chain C: G.120, L.295 No protein-ligand interaction detected (PLIP) XE.8: 2 residues within 4Å: Chain D: G.120, L.295 No protein-ligand interaction detected (PLIP) XE.10: 1 residues within 4Å: Chain E: G.120 No protein-ligand interaction detected (PLIP) XE.12: 1 residues within 4Å: Chain F: F.313 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Malashkevich, V.N. et al., Crystal structure of glutamate decarboxylase beta from Escherichia coli: complex with xenon. To be Published

Release Date

2009-02-03

Peptides

Glutamate decarboxylase beta: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

Glutamate decarboxylase beta

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